MonaLisa is a Petri net based tool for the analysis of biochemical networks. It comprises an editor supported by an intuitive visualization and animation, and various analysis techniques, focusing on network decomposition, knockout analysis, and other. It includes the computation of elementary modes (T-invariants), P-invariants, Maximal common transition sets (MCT-sets), T-clusters, minimal cut sets (MCS), degree distribution, cluster coefficient distribution.

The figure depicts the graphical user interface (GUI) of MonaLisa. On the left side, the analytical part of MonaLisa is shown. Here, the user can
select the approaches, define the settings, export the results and/or the PN in different formats. In the middle, the NetViewer represents the PN model of
the carbon metabolism of sucrose breakdown pathway in the potato tuber (Koch et al., 2005). The metabolites (places) are drawn as circles and the reactions
(transitions) as rectangles. The gray-filled circles indicate clone markers (logical places), i.e. those with equal names occur only once in the underlying graph.
The color highlighting indicates all transitions of a single elementary mode/transition invariant, including the corresponding pre- and post-places. On the right
side, the ToolBar with all modeling and visualization settings is depicted. The shown menu controls the highlighting of elementary modes, place invariants,
and maximal common transition sets. The elementary modes can be divided into several categories like those which are cyclic or have only an input but no
output and vice versa.

Download & License

This program is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
FOR A PARTICULAR PURPOSE.

A documentation of MonaLisa is available online. For a quickstart guide see below.

Quickstart

To use MonaLisa you have to install Java 6 or higher. To install MonaLisa you have to extract the archive in an arbitrary folder. The archive contains a folder lib with all libraries. This folder must be located in the same folder as MonaLisa.jar. To start MonaLisa just perform a double click on the MonaLisa.jar. If jar files not linked to Java, you need to execute MonaLisa out of your console using the following command:

java -jar /PATH/TO/MONALISA/MonaLisa.jar

For big networks, you have to start MonaLisa with more memory for the Java virtual machine: